Current methods of understanding microbiome composition and structure rely on accurately estimating the number species and their relative abundance. Most of these methods require an efficient PCR whose forward and reverse primers bind well to the same, large number of identifiable species, and produce amplicons that are unique. It is therefore not surprising that currently used universal primers designed many years ago are not as efficient and fail to bind to recently cataloged species. We propose an automated general method of designing PCR primer pairs that abide by primer design rules and since the method is automated, primers can be designed for targeted groups of microbial species or updated when a database is updated. In silico experiments and laboratory experiments confirm the efficacy of the newly designed primers for metagenomics applications.